Extinction

Extinction is final: absent leaps in genomic engineering, once a species is gone it is gone for good. The extinction crisis of the modern era was a key motvation for the ESA (CITES): the goals of the law include preventing extinction and recovering species so they are no longer threatened with extinction. One of the ways the success of the ESA is measured is by comparing the number of listed species to the number that are extinct. As of this writing, ten species have been removed from the list of threatened and endangered species, and the list includes 1,652 species. Those numbers suggest 99.4% of species have been saved by the ESA, which by any means is a superb accomplishment.

There are a few problems with using the number of species “delisted due to extinction” as the metric of success. First, it ignores the key goal of species recovery and uses the lower bar of mere existence as success. But would anyone really argue that plants and animals known only to exist in captivity count as successes?

Second, we know that the ten delisted species are simply the ones formally accepted as extinct. But proving extinction is tough; we have too many examples where a species hadn’t been seen for many, many years–multiple decades and even over a century–only to be rediscovered (CITES). For such reasons, declarations of extinction are a rare occurrence. At the same time, we often have a darn good idea that well-documented species are really-and-truly extinct. We hold off on the declarations of extinction and the removal of protections because of the small but real chance that one or a few individuals still exist.

My goal here is to find the species that experts - biologists with the U.S. Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS; collectively, the Services) - have good reason to believe are or may be extinct. Declaring extinction may not be warranted for many or most of these, but these professionals have indicated that extinction is likely to some greater or lesser degree. Getting a better handle on the number of species thought to be extinct rather than relying on the number delisted due to extinction is an essential component to understanding the effectiveness of the ESA.

Identifying possible/probably extinctions

The first question we address is how many species are extinct. Pinning down that number is tricky because extinction is fundamentally hard because proving absence is so difficult (CITES). Rather than a declaration of extinct, we set the bar at a level of experts’ statements that they think the species is or may be extinct. From among the ~1,400 five-year reviews, totalling >30,000 pages, we need to find a relatively small number of phrases that indicate extinction. We used a set of seven regular expression patterns as a coarse filter:

  1. "(possibly|may be|have become) extinct"
  2. "(certainly being|probably|is|likely|probably being) extinct"
  3. "no (populations|individuals)( are)* known"
  4. "no( known| living)* individuals"
  5. "extinct in( the)* wild"
  6. "last (seen|observed|found) in [0-9oOiI]+"
  7. "functionally extinct"

In these patterns, “|” means “or” for the set of words inside parentheses. For example, the first pattern would match “possibly extinct,” “may be extinct,” or “have become extinct.” The “*" means the preceding letter or word matches zero or more times, whereas “+” means the preceding word/letter(s) must match one or more times. We checked all seven patterns against all 1,385 five-year reviews we collected from ECOS and NMFS’s recovery site.

This search returned 387 matches to the patterns, with pattern six (“last seen in…”) most common:

pattern n
1 44
2 59
3 3
4 125
5 21
6 128
7 7

A few examples of sentences in which pattern six was found include:

  • the subspecies may no longer be present in the laguna mountains, which was the original type location for the subspecies, as it was last seen in 1999 (pratt 1999).
  • however, because the maryland darter was last observed in 1938, an assessment of the darter’s status is best seen in light of the longer history of surveys for this species.
  • the diesel occurrence was last seen in 1980 and is considered extirpated due to development activities.
  • herbarium records indicate this site was last found in 1931 and was located approximately two miles east of the town of keno, oregon.
  • this population was about 8 miles (13 kilometers) from the nearest known occurrence, which consisted of a single plant last seen in 1984.
  • on lanai, the taxon was last seen in 1929, but its habitat remains threatened by axis deer, mouflon sheep (factors a and d), and invasive introduced plant species (factor e) (usfws 2003a).
  • dade rice glade / ozark first and last observed in 1989 private / not protected.
  • eo rank = c 2,215 plants polk eudora glades / ozark first observed in 1970 private / registered by tnc in 1980s but no walnut grove last observed in 1984 enforceable protection.
  • eo rank = c ^larkansas natural county site name/quad division collection/observation data ownership/comments bradley & warren prairie west gulf first observed in 1958 anhc / most subpopulations observed casually in drew natural area / coastal last observed in 2006 2006.
  • cleveland kingsland prairie / west gulf first observed in 1982 tnc and private / all known plants occur on tnc- new edinburg coastal last observed in 2006 owned portion of prairie.

And examples of pattern two (higher likelihood of extinction) matches include:

  • in november and december of 2006, a visual and acoustic survey failed to locate a single baiji leading to conclusions that the baiji is likely extinct (turvey 2008; turvey et al.
  • 1.3.4 review history monk seal 5-year review: november 9, 1984 a caribbean monk seal 5-year review published on november 9, 1984, determined that the best available information indicated the caribbean monk seal is extinct.
  • based upon our review of the status of this species, we conclude that the caribbean monk seal is extinct, primarily due to human exploitation.
  • 3.3 listing and reclassification priority number: _ 1 delisting priority number: 6 1 4.0 recommendations for future actions this status review concludes the caribbean monk seal is extinct.
  • the caribbean monk seal is extinct.
  • by the early 1980’s, palos verdes blue butterflies were found at only 10 locations (arnold 1987), and none were observed between 1983 and 1993, leading to the conclusion that the palos verdes blue butterfly was likely extinct (arnold 1987; mattoni 1992).
  • gary vinyard (1984), which attributed this extinction to limited distribution, habitat disturbance, and introductions of nonnative fishes.
  • a project has been funded by a service endangered species act section 6 grant to develop a protocol to estimate san diego fairy shrimp population sizes and conduct population viability analyses in real time, in order to detect a decline preceding the likely extinction of a population.
  • this taxon has not been collected in more than 70 years and is likely extinct.
  • 2.3.1.5 spatial distribution, trends in spatial distribution (e.g. increasingly fragmented, increased numbers of corridors, etc.), or historic range (e.g. corrections to the historical range, change in distribution of the species’ within its historic range, etc.): -4- ^l at the time it was listed, the little mariana fruit bat had last been observed in the 1960s, and the species has been considered as likely extinct since the time of the recovery plan’s publication in 1990.

Perusing the pattern matches, we find (as expected) both true positives (i.e., the meaning of the matched sentence comports with the idea we have in mind) and false positives (e.g., local extinctions or species previously believed extinct but since re-discovered). We also recognize that the current table doesn’t identify the (one or more) species in each document. After joining the pattern matches with a table that links five-year review documents and species (scientific names), we manually checked each of the 221 five-year reviews with matches to # filter out the false-positives.

From the manually filtered data we find 46 species that are believed extinct to some greater or lesser degree, plus the snail genus Achatinella. There were 41 species listed in the snail genus and a number - somewhere between 15 and 30 species, though it is difficult to tell exactly how many - are thought to be extinct.

Acaena exigua
Achatinella spp.
Akialoa stejnegeri
Amaranthus brownii
Anolis roosevelti
Cyanea copelandii ssp. copelandii
Cyanea superba
Cyrtandra crenata
Delissea rhytidosperma
Dipodomys heermanni morroensis
Eleutherodactylus jasperi
Epioblasma torulosa torulosa
Erimystax cahni
Etheostoma sellare
Hemignathus hanapepe
Hibiscadelphus giffardianus
Hibiscadelphus hualalaiensis
Hibiscadelphus woodii
Kadua degeneri
Loxops ochraceus
Melamprosops phaeosoma
Melicope quadrangularis
Moho braccatus
Myadestes lanaiensis rutha
Myadestes myadestinus
Numenius borealis
Obovaria retusa
Ochrosia kilaueaensis
Paroreomyza flammea
Paroreomyza maculata
Phyllostegia glabra var. lanaiensis
Phyllostegia kaalaensis
Phyllostegia mollis
Pleurobema curtum
Pleurobema marshalli
Polygyriscus virginianus
Psittirostra psittacea
Pteropus tokudae
Puma (=Felis) concolor couguar
Quadrula stapes
Rallus owstoni
Rana sevosa
Rorippa gambellii
Tetramolopium capillare
Zosterops conspicillatus conspicillatus

Together with the ten species that have been delisted due to extinction, we estimate 70-85 (4 - 5%) current or formerly ESA-listed species are believed, to some greater or lesser extent, to be extinct.

We address the geography of extinctions below, but note here that most of these species are from Hawaii and many of those are plants (Box 1).

Box 1. Complementary data from PEP

The Plant Extinction Prevention (PEP) Program works exhaustively to monitor and conserve Hawaiian plants. They also provide more up- to-date data on the status of many imperiled plants than FWS documents, and should probably be considered authoritative for PEP species.

We downloaded the 2017-03-16 list from PEP’s website then used Adobe’s online extraction service to render the tables as a spreadsheet for processing. To begin, we have a high-level overview of how PEP classifies the covered species:

PEP_class n
N/A 1
PEP 227
PEP-Extinct in Wild 14
PEP-EXTINCT? 20
PEP-EXTIRPATED 45
PEP-Extirpated in Wild 3
PEP-EXTIRPATED? 14

Appropriately, PEP uses “?” to denote species for which extirpation and extinction are unknown. The refinement of extinct in the wild vs. extinct from the planet is also useful to consider. Last, in addition to the extinctions, the PEP data highlight the problem of extirpations: 34 PEP species have been (or probably have been) extirpated from one or more of the islands. First, the number of extirpations by island:

extirpations
Maui 14
Molokai 14
Lanai 10
Kauai 7
Oahu 5
Hawaii 4
Niihau 4
Kahoolawe 1

And second, by most species:

extirpations
Scaevola coriacea 5
Adenophorus periens 4
Diplazium molokaiense 4
Isodendrion pyrifolium 4
Canavalia pubescens 3
Acaena exigua 2
Asplenium dielerectum 2
Brighamia rockii 2
Deparia kaalaana 2
Gardenia brighamii 2

The PEP data adds depth to our understanding of extinctions and extirpations among Hawaiian plants, but PEP doesn’t cover all ESA-listed plants. By combining PEP table with county occurrence data, we find 320 species are not covered by PEP; more are missing than are covered by PEP. For these species in particular it is important for FWS to track species status. One way that is done is with ESA-mandated five-year reviews of species status.

There are 279 non-PEP species with 5-year reviews available, and of those reviews, 200 are out-of-date (i.e., more than five years old).

Geography of extinctions

state n
Hawaii 24
Mississippi 5
Alabama 4
Guam 3
Tennessee 3
Virginia 3
California 2
Kentucky 2
Maryland 2
West Virginia 2

state_county n
Honolulu, Hawaii 8
Kauai, Hawaii 7
Maui, Hawaii 7
Hawaii, Hawaii 5
NA, NA 4
Guam, Guam 3
Bedford, Tennessee 2
Bland, Virginia 2
Blount, Tennessee 2
Buchanan, Virginia 2
Butler, Kentucky 2
Claiborne, Tennessee 2
Colbert, Alabama 2
Dickenson, Virginia 2
Edmonson, Kentucky 2

Common threats and habitats